Showing : scRNAseq • reset
1
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Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 7 days ago by ★ 4.0k • written 3 months ago by • 0
0
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1
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183
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Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
updated 10 days ago by ★ 4.0k • written 17 days ago by • 0
0
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1
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262
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Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
updated 10 days ago by ★ 4.0k • written 3 months ago by • 0
5
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13
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1.2k
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Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 9 weeks ago by 53k • written 11 weeks ago by • 0
1
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2
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343
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Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 3 months ago by 53k • written 3 months ago by • 0
0
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11
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926
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emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn 10x scRNAseq emptyDrops DropletUtils
3 months ago Peter Hickey ▴ 760
0
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3
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993
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 months ago by 43k • written 9 months ago by • 0
0
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0
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404
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Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
9 months ago Muhammad • 0
0
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3
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861
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 9 months ago by • 0 • written 10 months ago by ▴ 10
2
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2
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845
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 15 months ago by ▴ 10
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0
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848
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Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
17 months ago Damini • 0
1
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8
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1.9k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 16 months ago by 53k • written 17 months ago by • 0
0
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0
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649
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
18 months ago Bibi • 0
0
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1
reply
991
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
0
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2
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1.1k
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Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
20 months ago rocanja ▴ 60
0
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1
reply
751
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How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
1
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2
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2.0k
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ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
24 months ago ruba-mahmoud • 0
0
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2
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1.4k
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scRNA analysis : DEG between low and high-expressing cells
scRNAseq
2.2 years ago Momo • 0
0
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1
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864
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FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
2
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5
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1.8k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.3 years ago duez.tolga • 0
0
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1
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2.8k
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DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
4
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3
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1.7k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
0
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1
reply
943
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If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
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1
reply
993
views
library(topGO) query
topGO scRNAseq
updated 2.4 years ago by ▴ 780 • written 2.4 years ago by • 0
0
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0
replies
793
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adding noise to scRNA Seq counts
scRNAseq
2.4 years ago Jiyuan • 0
1
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11
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9.5k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 2.1 years ago by • 0 • written 2.4 years ago by • 0
2
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3
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2.1k
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P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
2.5 years ago Lluís Revilla Sancho ▴ 760
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0
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1.0k
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News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
2.5 years ago info ▴ 10
0
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1
reply
1.1k
views
scRNAseq Download Errors
scRNAseq
updated 2.6 years ago by 4.2k • written 2.6 years ago by ★ 1.6k
2
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0
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2.6k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
2.6 years ago Tadeoye ▴ 20
0
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1
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1.6k
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scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.7 years ago by ▴ 760 • written 2.7 years ago by ▴ 10
4
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5
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2.9k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 2.7 years ago by ▴ 760 • written 2.7 years ago by ▴ 10
0
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2
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1.7k
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Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 2.1 years ago by • 0 • written 2.7 years ago by • 0
0
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3
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2.3k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 16 months ago by • 0 • written 3.0 years ago by • 0
1
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2
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2.0k
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What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
3.1 years ago Guandong Shang ▴ 40
1
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2
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1.5k
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Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
3.1 years ago evocanres • 0
0
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3
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1.8k
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scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
3.2 years ago • updated 3.1 years ago Madiha • 0
4
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5
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4.2k
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`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
3.3 years ago Peter Hickey ▴ 760
4
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2
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1.9k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
3.3 years ago Guandong Shang ▴ 40
0
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4
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3.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 3.3 years ago by ★ 29k • written 3.3 years ago by ▴ 40
0
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0
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1.5k
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Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
3.3 years ago peter.kharchenko ▴ 30
0
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0
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1.2k
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
3.4 years ago Sebastian Lewandowski • 0
1
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4
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2.0k
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Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
3.4 years ago Chise ▴ 10
0
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0
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1.7k
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how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
3.4 years ago Guandong Shang ▴ 40
0
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2
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2.7k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
0
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1
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1.8k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
2
votes
8
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2.6k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
3.4 years ago Kelen ▴ 10
0
votes
1
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1.2k
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 3.5 years ago by ▴ 780 • written 3.5 years ago by • 0
1
vote
2
replies
3.0k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
3.6 years ago Ismail • 0
1
vote
1
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2.9k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 3.7 years ago by ▴ 760 • written 3.7 years ago by • 0
96 results • Page 1 of 2
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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